Post-Translational Modifications on HLA Class I Presented Peptides

Caron Laboratory

Study Overview

This analysis characterizes post-translational modifications (PTMs) identified on HLA class I peptides from the JY cell line using data-dependent acquisition mass spectrometry. All analyses are restricted to peptides of length 8-14 amino acids.

HLA Alleles: A\*02:01, B\*07:02, C\*07:02

Data Summary

PTM Categories

HLA Binding Classification

Figure 1: PTM Composition

Figure 1A: PTM Distribution

Distribution of unique modified peptides by PTM type (length 8-14 amino acids).

Figure 1B: PTM Proportions

Proportional representation of each PTM class within the modified peptidome.

Figure 2: Peptide Length Distribution

Ridgeline density plot comparing peptide length distributions across PTM types. Gray distribution represents unmodified background peptides.

Figure 4A: PTM Landscape

Circos diagram illustrating relationships between PTM types (outer sectors), modified residues (links), and HLA binding alleles (inner elements). Link density reflects relative abundance of each PTM-residue combination.

Figure 4B: Positional Enrichment

By PTM and Residue

Log₂ enrichment of PTM occurrence at peptide positions 8-14 relative to background amino acid positional distribution. PTM+residue combinations with ≥20 occurrences. Color scale: blue (depletion) to red (enrichment), capped at ±3. Correlation column indicates similarity to background distribution.

By PTM Type (Aggregated)

Aggregated positional enrichment by PTM type (≥50 occurrences), combining all modified residues.

Figure 4C: PTM Position Density

Density curves showing modification site distribution across peptide positions 8-14. PTM+residue combinations with ≥50 modifications.

Figure 5A: HLA Binding Affinity

Strong Binders by PTM and Residue

Percentage of strong HLA binders (EL Rank < 0.5%) for each PTM+residue combination across alleles A0201, B0702, and C0702. Combinations with ≥10 peptides.

Weak Binders by PTM and Residue

Percentage of weak HLA binders (0.5% ≤ EL Rank < 2%) for each PTM+residue combination.

Strong Binders by PTM Type

Strong binder percentages aggregated by PTM type across alleles.

Weak Binders by PTM Type

Weak binder percentages aggregated by PTM type.

Figure 5B: EL Rank Distribution

EL Rank distribution comparison between modified peptides (colored outlines) and background unmodified peptides (gray) within the binder range (EL Rank 0-2). Dashed lines indicate strong binder (0.5%) and weak binder (2%) thresholds.

Figure 6: Specific PTM Analyses

Figure 6A: Doubly Phosphorylated Peptides

Site distribution for peptides carrying two or more phosphorylation sites.

Figure 6B: Ubiquitination Remnants

Comparison of ubiquitin remnant types following tryptic digestion: single glycine (G, +57 Da) versus diglycine (GG, +114 Da).

Figure 6C: Oxidation Classification

Classification of oxidized peptides: biological oxidation (P, I, L, Q, S, T, V, C, D, E, N, Y, G, K, R) versus artifact oxidation (M, W, H).

Figure 6D: Biological Oxidation by Residue

HLA binding classification for biologically oxidized peptides stratified by oxidized residue. Sorted by percentage of strong binders.

Figure 6D2: Biological Oxidation Heatmap

Strong binder percentages for biological oxidation cross-tabulated by residue and HLA allele.

Figure 6E: Glycan Complexity

N-glycosylation analysis stratified by glycan complexity (sum of monosaccharide units). Categories: Simple (1-3), Medium (4-8), Complex (9-15).

Figure 6E2: Glycan Types

Individual glycan structures with HLA binding classification, sorted by monosaccharide count.

Analysis Date: January 2026 | Made by: Peter Kubiniok